Main
Kasia Kedzierska
I am a 3rd year PhD student at the University of Oxford. I am a comuptational biologist, i.e. I use Data Science and Statistical Machine Learning while answering biological questions related to cancer of the uterus. Specifically, I study chromatin organisation in endometrial cancer. I spend most of my time either in command line writing Bash/Awk scripts or analysing and visualising data n R/Python.
I like teaching and deeply believe in Open Science. I am the President of #NGSchool Society with which I’ve been organising Summer Schoools in Bioinformatics. During last year edition - #NGSchool2019: Machine Learning for Biomedicine we recorded and published some of the lectures. This year, becasue of the pandemic we switched to organising virtual events, like NGSseminars series.
Research Experience
DPhil Candidate
Church group @ Wellcome Centre for Human Genetics, Wedge group @ Big Data Institute
University of Oxford, UK
2022 - 2018
- PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
Visiting Graduate Student
Ratan group
University of Virginia, USA
2018 - 2017
- Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
- Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.
Visiting Graduate Student
Pemberton group
University of Virginia, USA
2017 - 2016
- Worked on Epigenetic regulation in prostate cancer.
- Performed experiments and analyzed data from RNA-seq, ATAC-seq, and ChIP-seq assays.
Research Assistant
Zebrafish Developmental Genomics
IIMCB, Warsaw, Poland
2016 - 2015
- I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
- I was responsible for both computational and experimental aspects of the project.
Education
DPhil. Candidate, Genomic Medicine and Statistics
Nuffield Department of Medicine, Brasenose College
University of Oxford, UK
2022 - 2018
- Project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer.
- Wellcome Trust Studentship
M. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2018 - 2015
- Thesis: Analysis of the mutational burden across gene sets in cancer.
- Thesis awarded the best Master thesis in Bioinformatics defended in 2018 title.
B. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2015 - 2011
Publications
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
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2020
- MLH1 promoter polymorphism, rs1800734, association with MSI EC risk.
Prognostic integrated image-based immune and molecular profiling in early-stage Endometrial Cancer
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2020
- Quantification of intraepithelial CD8+ cells improved upon the prognostic utility of the molecular EC classification in early-stage EC
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
Genome Research
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2019
- Regulation networks in heart developmnent in zebrafish.
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
BMC Cancer
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2018
- DNA repair genes and androgen signalling in prostate cancer cell lines.
SONiCS: PCR stutter noise correction in genome-scale microsatellites
Bioinformatics
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2018
- Tool for genotyping short tandem repeats (STRs) profiled using capture assays, github.com/kzkedzierska/sonics
Posters, and Talks
Analysis of the mutational burden across gene sets in cancer
Polish Bioinformatics Society Symposium
Cracow, Poland
2019
- Invited talk
Differential mutation analysis across gene sets in cancers
The Biology of Genomes 2018
Cold Spring Harbor, NY, USA
2018
- Poster
Epigenetic regulation of prostate cancer
Visiting Graduate Traineeship Program Grantees Symposium
Charlottesville, VA, USA
2017
- Talk
Awards and honours
Best Master Thesis in Bioinformatics
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2019 - 2018
- The Best Master Thesis defended in the field of Bioinformatics in 2018 in Poland.
- Analysis of the mutational burden across gene sets in cancer Masther thesis defended at the Warsaw University of Technology; code for the analyses can be accessed github.com/kzkedzierska/cancers
Visiting Graduate Traineeship Program
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2017 - 2016
- The Visiting Research Graduate Traineeship Program offered 12-month research traineeships for outstanding, qualified students from the life sciences at selected institutions in the United States.
Grasz o Staz
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2015
- “Grasz o Staz” competition was a national, prestigious and highly competitive (1:25 success rate) scholarship program in Poland organized by PwC.
Teaching Experience
Online tutorials: Python for Data Science and Introduction to Python
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2020
- I led two Python tutorials: Introduction to Python kasia.codes/talk/intro_to_python/ and Python for Data Science kasia.codes/talk/py4ds/.
Introduction to Managing Code with Git
Wellcome Centre for Human Genetics
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2020 - 2019
- I led a 2-hour introduction to working with Git. The session aims at highlighting the advantages of working with Git as well as providing participants knowledge how to use Git.
Unsupervised learning, Introduction to Python
#NGSchool2019: Machine Learning for Biomedicine
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2019
- Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
- Materials for the Introduction to Python are available on github
Introduction to R
Wellcome Centre for Human Genetics
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2019
- 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
- Materials available on github/kzkedziersa/r_intro
ATAC-seq workshop
#NGSchool2017: Single-cell Sequencing
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2017
- Invited speaker
- Materials for the course can be available on gitub.com/kzkedzierska/ATACseq_workshop
Attended Workshops, Summer Schools
Machine Learning Summer School
Imperial College London, University College Londn
London, United Kingdom
2019
- 12-day intensive course on a variety of topics in machine learning.
Grants
Visegrad Grant to organize #NGSchool2020 - postponed until 2021
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2021 - 2020
- A platform to share expertise in the field of Next Generation Sequencing data analysis and general bioinformatics.
Visegrad Grant to organize #NGSchool2019
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2019
- 23,500 EUR awarded towards organising #NGSchool2019 allowed to keep the cost of attenting the school to the minimum and record the lectures for broader access.
Non profit work
President
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2021 - 2018
- The goal of the Society is to promote and support science, with emphasis on computational biology.
- President since 2019; Vice President 2018 - 2019